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Seed coat mediated resistance against Aspergillus flavus infection in peanut
Get PDFToxic metabolites known as aflatoxins are produced via certain species of the Aspergillus genus, specifically A. flavus, A. parasiticus, A. nomius, and A. tamarie. Although various pre- and post-harvest strategies have been employed, aflatoxin contamination remains a major problem within peanut crop, especially in subtropical environments. Aflatoxins are the most well-known and researched mycotoxins produced within the Aspergillus genus (namely Aspergillus flavus) and are classified as group 1 carcinogens. Their effects and etiology have been extensively researched and aflatoxins are commonly linked to growth defects and liver diseases in humans and livestock. Despite the known importance of seed coats in plant defense against pathogens, peanut seed coat mediated defenses against Aspergillus flavus resistance, have not received considerable attention. The peanut seed coat (testa) is primarily composed of a complex cell wall matrix consisting of cellulose, lignin, hemicellulose, phenolic compounds, and structural proteins. Due to cell wall desiccation during seed coat maturation, postharvest A. flavus infection occurs without the pathogen encountering any active genetic resistance from the live cell(s) and the testa acts as a physical and biochemical barrier only against infection. The structure of peanut seed coat cell walls and the presence of polyphenolic compounds have been reported to inhibit the growth of A. flavus and aflatoxin contamination; however, there is no comprehensive information available on peanut seed coat mediated resistance. We have recently reviewed various plant breeding, genomic, and molecular mechanisms, and management practices for reducing A. flavus infection and aflatoxin contamination. Further, we have also proved that seed coat acts as a physical and biochemical barrier against A. flavus infection. The current review focuses specifically on the peanut seed coat cell wall-mediated disease resistance, which will enable researchers to understand the mechanism and design efficient strategies for seed coat cell wall-mediated resistance against A. flavus infection and aflatoxin contamination
Exported J domain proteins of the human malaria parasite
Get PDFThe heat shock protein 40 (Hsp40) family, also called J domain proteins (JDPs), regulate their Hsp70 partners by ensuring that they are engaging the right substrate at the right time and in the right location within the cell. A number of JDPs can serve as co-chaperone for a particular Hsp70, and so one generally finds many more JDPs than Hsp70s in the cell. In humans there are 13 Hsp70s and 49 JDPs. The human malaria parasite, Plasmodium falciparum, has dedicated an unusually large proportion of its genome to molecular chaperones, with a disproportionately high number of JDPs (PfJDPs) of 49 members. Interestingly, just under half of the PfJDPs are exported into the host cell during the asexual stage of the life cycle, when the malaria parasite invades mature red blood cells. Recent evidence suggests that these PfJDPs may be functionalizing both host and parasite Hsp70s within the infected red blood cell, and thereby driving the renovation of the host cell towards pathological ends. PfJDPs have been found to localize to the host cytosol, mobile structures within the host cytosol (so called “J Dots”), the host plasma membrane, and specialized structures associated with malaria pathology such as the knobs. A number of these exported PfJDPs are essential, and there is growing experimental evidence that they are important for the survival and pathogenesis of the malaria parasite. This review critiques our understanding of the important role these exported PfJDPs play at the host-parasite interface
Functional and structural consequences of TBK1 missense variants in frontotemporal lobar degeneration and amyotrophic lateral sclerosis
No full textMutations in the Tank-binding kinase 1 (TBK1) gene were identified in 2015 in individuals with frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). They account for ∼3–4% of cases. To date, over 100 distinct mutations, including missense, nonsense, deletion, insertion, duplication, and splice-site mutations have been reported. While nonsense mutations are predicted to cause disease via haploinsufficiency, the mechanisms underlying disease pathogenesis with missense mutations is not fully elucidated. TBK1 is a kinase involved in neuroinflammation, which is commonly observed in these diseases. TBK1 also phosphorylates key autophagy mediators, thereby regulating proteostasis, a pathway that is dysregulated in ALS-FTLD. Recently, several groups have characterised various missense mutations with respect to their effects on the phosphorylation of known TBK1 substrates, TBK1 homodimerization, interaction with optineurin, and the regulation of autophagy and neuroinflammatory pathways. Further, the effects of either global or conditional heterozygous knock-out of Tbk1, or the heterozygous or homozygous knock-in of ALS-FTLD associated mutations, alone or when crossed with the SOD1G93A classical ALS mouse model or a TDP-43 mouse model, have been reported. In this review we summarise the known functional effects of TBK1 missense mutations. We also present novel modelling data that predicts the structural effects of missense mutations and discuss how they correlate with the known functional effects of these mutations
Getting the best from pot trials with soil-borne Oomycetes
Get PDFSoil-borne Oomycetes are important pathogens of nursery plants, agricultural and horticultural crops, and woody plants in natural ecosystems. They are most damaging when plants are overwatered or growing in poorly drained sites. Poor growth could result from root infection, root damage resulting from the anoxic conditions which develop in saturated soil, or both. This is essential information for devising appropriate management options, as these will differ depending on the primary cause of poor health. Pot experiments are often used to determine whether these soil-borne pathogens cause root infection which is assumed to be by zoospores produced in wet soil. Soil saturation followed by draining, is included as part of the experimental protocol to generate zoospores from the inoculum and facilitate their movement to, and infection of, plant roots. However, if soil saturation persists until the soil becomes anoxic, this may affect the host. In our opinion, this can muddle the interpretation of results, unless there are adequate controls which include root infection in unsaturated soil, and the effect of soil saturation on the host in the absence of the pathogen. Pot experiments are expensive in both time and equipment. They must be conducted to provide clear answers to the postulated hypotheses and ensure experiments are repeatable. We provide guidelines for conducting such pot experiments which will assist in clarifying the roles of these pathogens and soil saturation on plant growth, both separately and in combination
Chasing flies: The use of wingbeat frequency as a communication cue in calyptrate flies (Diptera: Calyptratae)
Get PDFThe incidental sound produced by the oscillation of insect wings during flight provides an opportunity for species identification. Calyptrate flies include some of the fastest and most agile flying insects, capable of rapid changes in direction and the fast pursuit of conspecifics. This flight pattern makes the continuous and close recording of their wingbeat frequency difficult and limited to confined specimens. Advances in sound editor and analysis software, however, have made it possible to isolate low amplitude sounds using noise reduction and pitch detection algorithms. To explore differences in wingbeat frequency between genera and sex, 40 specimens of three-day old Sarcophaga crassipalpis, Lucilia sericata, Calliphora dubia, and Musca vetustissima were individually recorded in free flight in a temperature-controlled room. Results showed significant differences in wingbeat frequency between the four species and intersexual differences for each species. Discriminant analysis classifying the three carrion flies resulted in 77.5% classified correctly overall, with the correct classification of 82.5% of S. crassipalpis, 60% of C. dubia, and 90% of L. sericata, when both mean wingbeat frequency and sex were included. Intersexual differences were further demonstrated by male flies showing significantly higher variability than females in three of the species. These observed intergeneric and intersexual differences in wingbeat frequency start the discussion on the use of the metric as a communication signal by this taxon. The success of the methodology demonstrated differences at the genus level and encourages the recording of additional species and the use of wingbeat frequency as an identification tool for these flies
eDNA metabarcoding shows latitudinal eukaryote micro- and mesoplankton diversity stabilizes across oligotrophic region of a >3000 km longitudinal transect in the Indian Ocean
No full textSea surface planktonic assemblages were sampled using environmental DNA at 1.5° latitudinal increments (from 39.5 to 11.5°S) following the 110°E meridian in the Eastern Indian Ocean to reveal factors structuring eukaryotic diversity. Metabarcoding the v4 region of the 18S rRNA gene revealed a eukaryotic assemblage over-dominated by amplicon sequence variants representing just four taxa that comprised 50% of reads, which were from copepods. Eukaryotes were predominantly heterotrophs and mixotrophs, with the presence of individual taxa responding to nutrient and temperature/oxygen gradients. Assemblage richness and diversity was greater at the northern end of the transect, but this diversity change occurred mostly around the sub-tropical front (∼35°S) with an unusually high degree of uniformity and non-monotonic progression in the alpha and beta diversity over the majority of the transect despite extending through distinct water masses, i.e., Indonesian Throughflow with tropical, low salinity waters, Subtropical Surface Water of high salinity waters and varying temperature, and Sub-Antarctic Mode Water with cooler and low salinity water. However, piecewise linear models of environmental and biotic data and fuzzy c-means clustering (with k = 2, 3 or 4) identified some discontinuities in the transect that were clumped at the southern end of the transect, although these cluster boundaries lacked consensus, being often poorly defined between the different data types. This eDNA data was largely concordant with morphological analyses, that also found the eukaryotic assemblage became largely stable northwards of the southernmost sampling points. These results contrast to other observations of diversity increasing monotonically toward the equator; i.e., eukaryotic communities were contrary to the “latitudinal diversity gradient hypothesis”. This accords with observations that extremely oligotrophic conditions can stabilise planktonic assemblages, despite significant latitudinal differences in temperature of as much as 16 °C
Decoding the formation of diverse petal colors of Lagerstroemia indica by integrating the data from transcriptome and metabolome
Get PDFLagerstroemia indica has great economic value due to its ecological, medicinal, and ornamental properties. Because its bloom color is one of the most essential characteristics, research into its color development is a hot topic. In this study, five representative colored cultivars were chosen, each representing a different color, such as white, red, pink, violet, and purple. Fully bloomed flowers were used to detect flavonoids in the petals. Anthocyanin is the main factor for the color formation of L. indica. 14 anthocyanins were discovered among the 299 flavonoids. Among 14 anthocyanins, malvidin-3,5-di-O-glucoside varied greatly among four colored samples and is the main contributor to color diversity. Transcriptome sequencing revealed that compared to white flowers, Anthocyanin pathway genes appear to be more active in colored samples. Analyzing the correlation network between metabolites and differential expressed genes, 53 key structural genes, and 24 TFs were detected that may play an essential role in the formation of color in L. indica flowers. Among these, the differential expression of F3′5′H and F3′H between all samples are contributors to color diversity. These findings lay the foundation for discovering the molecular mechanism of L. indica flower color diversity
Exploring the multi-level perspective in municipal solid waste management transition
No full textThe successful transition of municipal solid waste management (MSWM) in low-income economies towards a more sustainable practice is dependent on socio-political drivers, enablers/interventions, and service delivery practices. However, Environmental and sustainability sub-components influence this transition initiatives regarding sustainable MSWM. Informed by the theory of Multi-Level Perspective (MLP), we developed a nuanced Dimensional Evaluation of Waste Transition (DEWasT) model for MSWM to clarify societal factors and triggers for sustainability. This model elucidates the transition of MSWM, characterised by the three-level MLP, namely, landscape pressures, regimes, and niche innovations. The interaction of these transition levels within this model allows policymakers, institutions, and stakeholders to understand the current structure and dynamics. It will enable practical guidelines for MSWM sustainability practices, influencing a paradigm change towards MSWM innovations in low-income economies and closing the gaps identified by previous practitioners
Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9
Get PDFCRISPR-mediated genome editing has become a powerful tool for the genetic modification of biological traits. However, developing an efficient, site-specific, gene knock-in system based on homology-directed DNA repair (HDR) remains a significant challenge in plants, especially in woody species like poplar. Here, we show that simultaneous inhibition of non-homologous end joining (NHEJ) recombination cofactor XRCC4 and overexpression of HDR enhancer factors CtIP and MRE11 can improve HDR efficiency for gene knock-in. Using this approach, the BleoR gene was integrated onto the 3′ end of the MKK2 MAP kinase gene to generate a BleoR-MKK2 fusion protein. Based on fully edited nucleotides evaluated by TaqMan real-time PCR, the HDR-mediated knock-in efficiency was up to 48% when using XRCC4 silencing incorporated with a combination of CtIP and MRE11 overexpression compared with no HDR enhancement or NHEJ silencing. Furthermore, this combination of HDR enhancer overexpression and NHEJ repression also increased genome targeting efficiency and gave 7-fold fewer CRISPR-induced insertions and deletions (InDels), resulting in no functional effects on MKK2-based salt stress responses in poplar. Therefore, this approach may be useful not only in poplar and plants or crops but also in mammals for improving CRISPR-mediated gene knock-in efficiency
Developing of molecular therapies for collagen 3A1 mutations: Ehlers-Danlos syndrome
Get PDFVascular Ehlers-Danlos syndrome or Ehlers-Danlos syndrome type IV (vEDS), a connective tissue disorder characterized by skin hyperextensibility, joint hypermobility and fatal vascular rupture, is caused by COL3A1 mutations that disrupt collagen III expression and structure. Collagen III is a fibrillar collagen and, along with collagens I, II, V and XI, plays an important role in the extracellular matrix (ECM), particularly in the inner organs. To date, only symptomatic treatment for vEDS patients is available. Fibroblasts derived from vEDS patients carrying dominant negative and/or haploinsufficiency mutations in COL3A1 demonstrated reduced collagen III deposition in the ECM, presumably due to compromised COL3A1 homo-trimer fibril assembly. The study explored the potential of an antisense oligonucleotide (AO) mediated splice switching strategy to bypass COL3A1 mutations affecting in-frame exons. Antisense oligonucleotides, designed to redirect COL3A1 pre-mRNA processing to excise specific exons were transfected into vEDS patient and healthy control fibroblasts. Exons 10, 15 and 40 could be excised from the mature COL3A1 mRNA, although variable levels of exon skipping were observed in transfected patient fibroblasts. Intracellular collagen III expression was increased after AO transfection and induction of the internally truncated isoforms, leading to a reduction in collagen III deposition in the ECM, compared to that in sham and untreated fibroblasts as assessed by immunofluorescence staining. In conclusion, this study explored skipping of specific in-frame COL3A1 exons, as a potential therapy for selected vEDS cases. While efficient exon skipping, and therefore induced isoform generation was achieved, the resultant collagen III protein isoforms showed extracellular matrix defects. The outcome of altering collagen III repeat structure on trimerization suggests that newly induced collagen III isoforms missing only one exon will not tolerate such changes, and this therapeutic avenue does not appear viable for vEDS